CS 341: Systems Biology I

Software for Fall 2022

All the required software for this course is already installed on the Davis dwarves and in Davis 102. Use the below instructions to install the software on your personal computer. I am providing this information "as-is"; I cannot support/debug installation issues.

Python

These instructions were originally written for Python 3.7, but should work for more recent releases. If you already have Python 3.X with numpy, scipy, matplotlib, and Jupyter notebooks, then you probably don't need to update the installation (the only exception might be that scipy.integrate.solve_ivp is new, but if you don't have it, you can use scipy.integrate.odeint).

Python 3.X (Windows)

1. Download Latest Python 3 Release and run the installer.
2. Make sure the last checkbox is checked: "Add Python 3.X to PATH".
3. Click "Install Now" at the top.
4. Press WinKey+R to open the Run box.
5. Type cmd and enter.
6. Type py --version and it should print Python 3.8.5. If it doesn't, something went wrong.

Python 3.X (macOS)

• Stephanie went to https://www.python.org/downloads/, pressed the "Download Python 3.8.5" button and was able to install it without using a Terminal. As of Sept 2022, the button says "Python 3.10.7", but Stephanie isn't updating her own machine because the current version isn't broken.
• But here are Terminal instructions, if you want them.
  1. Open the Terminal app.
  2. Install Xcode Command Line Tools by entering the following command: xcode-select --install.
  3. Install the Homebrew package manager by copy-pasting the following into the terminal
     /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)".
     This allows you to install Python 3 from the terminal.
  4. Install Python 3 by entering the following into the terminal: brew install python3
• Regardless of house you install Python, check to see if Python 3 installed properly by entering the following into the terminal: python3 --version.
  It should return Python 3.X.X where X is the most recent version.

Pip Python modules

You will need a standard set of data science / machine learning Python libraries installed:

• pip3 install numpy
• pip3 install scipy
• pip3 install matplotlib
• pip3 install jupyter

Jupyter notebooks

After installing Jupyter notebook, follow the these steps to open and update a notebook file (.ipynb file extension).

1. Open terminal
2. Change directory to your project folder (e.g. with cd).
3. Enter the command jupyter notebook. A browser window should pop up with a file browsing interface of the current working directory in Terminal.
   Note that Stephanie had difficulty getting Jupyter to use Python 3.X (it kept opening in Python 2 mode), so she used the complete path to make sure it used the right version: /Library/Frameworks/Python.framework/Versions/3.8/bin/jupyter notebook. This was strange because if she typed which jupyter, she got the correct version.
4. Open a notebook file.
5. Execute cells with Shift+Enter. Make sure the notebook says "Trusted" on the top-right. If the notebook is not trust, click the Not Trusted button, then confirm that the notebook is safe.
6. Manually save frequently with Cmd+S